Hi Max,
1. If some net is our customer, have the agreement with us, but was NOT registered with our LIR - what we should do?
That should not be a problem. The end user needs to have a contract with an LIR. It does not really matter which LIR it is, and the user can move between LIRs if they want. They have a provider independent resource after all :)
2. The contract should include annual payments, and in good case we should put the actual sum inside the contract (instead of "please sign here you should pay wedontknowhowmuch later). The LIR billing scheme or even all the scheme candidates (I have to keep in mind the worst one for me when I deal with my users, of course) will appear later than we have to upload contracts.
A good idea would be to leave the exact amount out of the contract and specify that the fee depends on the fee the RIPE NCC charges you. That way you won't get into trouble when the fees change later. - Sander